Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012015.1 Corchorus olitorius cultivar O-4 contig12048, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 20367
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:53 original size:12 final size:11

Alignment explanation


    Indices: 36--70  Score: 52
    Period size: 12  Copynumber: 3.0  Consensus size: 11

         26 GAAGTAAAGT

                        
         36 TTAATTATATAA
          1 TTAATTA-ATAA

                        
         48 TTAATTAATATA
          1 TTAATTAATA-A

                       
         60 TTAATTAATAA
          1 TTAATTAATAA

         71 ATATTATAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  11    4  0.18
  12   18  0.82

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (11 bp):   
TTAATTAATAA

Found at i:64 original size:16 final size:17

Alignment explanation


    Indices: 36--79  Score: 58
    Period size: 16  Copynumber: 2.8  Consensus size: 17

         26 GAAGTAAAGT

                             
         36 TTAAT-TATATAATTAA
          1 TTAATATATATAATTAA

                             
         52 TTAATATAT-TAATTAA
          1 TTAATATATATAATTAA

             *           
         68 TAAATAT-TATAA
          1 TTAATATATATAA

         80 AAAATTAAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  15    1  0.04
  16   21  0.84
  17    3  0.12

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (17 bp):   
TTAATATATATAATTAA

Found at i:8576 original size:27 final size:27

Alignment explanation


    Indices: 8513--8580  Score: 91
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       8503 GATCATCGGC

                *                      
       8513 CTCCCTAGGTTCAGTCACCCCACCTAA
          1 CTCCTTAGGTTCAGTCACCCCACCTAA

            *    *       *             
       8540 GTCCTCAGGTTCATTCACCCCACCTAA
          1 CTCCTTAGGTTCAGTCACCCCACCTAA

               *          
       8567 CTCTTTAGGTTCAG
          1 CTCCTTAGGTTCAG

       8581 GGTACCAGTG


Statistics
Matches: 33,  Mismatches: 8, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  27   33  1.00

ACGTcount: A:0.21, C:0.38, G:0.13, T:0.28


Consensus pattern (27 bp):   
CTCCTTAGGTTCAGTCACCCCACCTAA

Found at i:17333 original size:25 final size:24

Alignment explanation


    Indices: 17287--17346  Score: 93
    Period size: 25  Copynumber: 2.4  Consensus size: 24

      17277 AATTAAGAAA

                                    
      17287 ATAATAATTATTTTTAGAATAATT
          1 ATAATAATTATTTTTAGAATAATT

                                     
      17311 ATAATAATTATTATTTAGAATAATT
          1 ATAATAATTATT-TTTAGAATAATT

                *      
      17336 ATTATTAATTA
          1 A-TAATAATTA

      17347 GTATATGCCG


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
  24   12  0.36
  25   13  0.39
  26    8  0.24

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (24 bp):   
ATAATAATTATTTTTAGAATAATT

Found at i:17339 original size:19 final size:19

Alignment explanation


    Indices: 17311--17347  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      17301 TAGAATAATT

                         *     
      17311 ATAATAATTATTATTTAGA
          1 ATAATAATTATTAATTAGA

                 *            
      17330 ATAATTATTATTAATTAG
          1 ATAATAATTATTAATTAG

      17348 TATATGCCGC


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49


Consensus pattern (19 bp):   
ATAATAATTATTAATTAGA
Done.